http://evolution.genetics.washington.edu/phylip/software.html

Here are some 194 of the phylogeny packages, and 16 free servers, that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made about twice a year (however, almost no updates have been made since the start of 2001, and this will continue until at least the end of 2002 when I hope to complete a major writing project). Some of these programs are available over Internet from ftp server machines, or by World Wide Web.

The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. I have listed as free those that I knew were free; for the others you have to ask their distributor.

If you discover any inaccuracies, or feel that I have left any important programs or facts out, or if links do not work properly, please e-mail me at: ( joe@genetics.washington.edu ).

... by methods available

... by computer systems on which they work

... cross-referenced by method and by computer system.

... by ones which analyze particular kinds of data.

... to show the most recent listings

... to show ones most recently changed

Phylogeny programs formerly listed here but no longer distributed

Which kinds of programs are and are not listed

Other lists of phylogeny software

• General-purpose packages
• Parsimony programs
• Distance matrix methods
• Computation of distances
• Maximum likelihood and related methods
• Quartets methods
• Artificial-intelligence methods
• Invariants (or Evolutionary Parsimony) methods
• Interactive tree manipulation
• Looking for hybridization or recombination events
• Bootstrapping and other measures of support
• Compatibility analysis
• Consensus trees and distances between trees
• Tree-based alignment
• Biogeographic analysis and host-parasite comparison
• Comparative method analysis
• Simulation of trees or data
• Examination of shapes of trees
• Clocks, dating and stratigraphy
• Description or prediction of data from trees
• Tree plotting/drawing
• Sequence management/job submission
• Teaching about phylogenies
• Web or e-mail servers that can analyze data for you

General-purpose packages

• PHYLIP
• PAUP*
• MEGA
• VOSTORG
• Fitch programs
• Phylo_win
• ARB
• DAMBE
• PAL
• Bionumerics

Parsimony programs

• PAUP*
• Hennig86
• MEGA
• Tree Gardener
• RA
• Nona
• PHYLIP
• TurboTree
• Freqpars
• Fitch programs
• CAFCA
• Phylo_win
• sog
• gmaes
• LVB
• GeneTree
• TAAR
• ARB
• DAMBE
• MALIGN
• POY
• DNASEP
• SEPAL
• Gambit
• TNT
• GelCompar II
• Bionumerics
• TCS

Distance matrix methods

PHYLIP PAUP* MEGA MacT ODEN Fitch programs ABLE TREECON DISPAN RESTSITE NTSYSpc METREE TreePack TreeTree GDA Hadtree, Prepare and Trees GCG Wisconsin Package SeqPup PHYLTEST Lintre WET Phylo_win njbafd Gambit gmaes DENDRON

Molecular Analyst Fingerprinting BIONJ TFPGA MVSP SOTA ARB BIOSYS-2 Darwin T-REX sendbs nneighbor DAMBE weighbor QR2 DNASIS minspnet PAL Arlequin vCEBL HY-PHY Vanilla GelCompar II Bionumerics qclust TCS

Computation of distances

PHYLIP PAUP* RAPDistance MULTICOMP MARKOV RSVP Microsat DIPLOMO OSA DISPAN RESTSITE NTSYSpc TREE-PUZZLE Hadtree, Prepare and Trees GCG Wisconsin Package AMP GCUA DERANGE2 POPGENE TFPGA REAP MVSP

SOTA RSTCALC Genetix BIOSYS-2 RAPD-PCR package DISTANCE Darwin sendbs K2WuLi GeneStrut Arlequin DAMBE DnaSP PAML puzzleboot MATRIX PAL Sequencer Vanilla GelCompar II Bionumerics qclust

Maximum likelihood and related methods

• PHYLIP
• PAUP*
• fastDNAml
• MOLPHY
• PAML
• Spectrum
• SplitsTree
• PLATO
• TREE-PUZZLE
• Hadtree, Prepare and Trees
• SeqPup
• Phylo_win
• PASSML
• ARB
• Darwin
• BAMBE
• DAMBE
• Modeltest
• TreeCons
• VeryfastDNAml
• PAL
• dnarates
• TrExMl
• HY-PHY
• Vanilla
• MEGA
• Bionumerics
• fastDNAmlRev
• RevDNArates
• rate-evolution
• MrBayes
• Hadtree, Prepare and Trees
• CONSEL

Quartets methods

• TREE-PUZZLE
• STATGEOM
• SplitsTree
• PHYLTEST
• GEOMETRY
• PICA95
• Darwin
• PhyloQuart
• Willson quartets programs
• Gambit

Artificial-intelligence methods

• SOTA

Invariants (or Evolutionary Parsimony) methods

• PHYLIP
• PAUP*

Interactive tree manipulation

• MacClade
• PHYLIP
• PDAP
• TreeTool
• ARB
• WINCLADA
• TreeEdit
• UO
• TreeExplorer
• TreeThief
• RadCon
• Mavric

Looking for hybridization or recombination events

• PLATO
• Bootscanning Package
• TOPAL
• reticulate
• RecPars
• partimatrix
• homoplasy test
• LARD
• Network
• TCS

Bootstrapping and other measures of support

PHYLIP PAUP* PARBOOT ABLE Random Cladistics AutoDecay TreeRot RASA DNA Stacks OSA DISPAN TreeTree PHYLTEST Lintre sog njbafd MEGA PICA95 ModelTest

TAXEQ2 BIOSYS-2 RAPD-PCR package TreeCons BAMBE DAMBE puzzleboot CodonBootstrap DNASEP SEPAL Gambit MEAWILK TrExMl Sequencer PAL PHYCON MrBayes CONSEL

Compatibility analysis

• COMPROB
• PHYLIP
• PICA95
• reticulate
• partimatrix
• SECANT
• CLINCH
• MEAWILK

Consensus trees and distances between trees

• COMPONENT
• TREEMAP
• NTSYSpc
• PHYLIP
• PAUP*
• REDCON
• TAXEQ2
• TreeCons
• QUARTET2
• RadCon

Tree-based sequence alignment

• TreeAlign
• ClustalW
• MALIGN
• GeneDoc
• GCG Wisconsin Package
• TAAR
• Ctree
• DAMBE
• POY
• ALIGN
• DNASIS

Biogeographic analysis and host-parasite comparison

• COMPONENT
• TREEMAP

Comparative method analysis

• PHYLIP
• CAIC
• COMPARE
• PA
• CMAP
• CoSta
• PDAP
• ACAP
• ANCML
• RIND
• MacroCAIC
• Fels-Rand
• Phylogenetic Independence

Simulation of trees or data

• COMPONENT
• Bi-De
• SEQEVOLVE
• TheSiminator
• Seq-Gen
• Treevolve and PTreevolve
• PSeq-Gen
• COMPARE
• ROSE
• PAML
• ProSeq
• PAL
• Vanilla

Examination of shapes of trees

• End-Epi
• MacroCAIC
• Genie
• PAL
• Vanilla
• RadCon
• BRANCHLENGTH

Clocks, dating and stratigraphy

• StratCon
• QDate
• Diversi
• K2WuLi
• Modeltest
• PAML
• TipDate
• RRTree
• vCEBL
• TreeEdit
• HY-PHY
• PAL
• rate-evolution
• BRANCHLENGTH

Description or prediction of data from trees

• CONSERVE
• TreeDis

Tree plotting/drawing

• PHYLIP
• PAUP*
• TreeTool
• TreeView
• Fitch programs
• NJplot
• DendroMaker
• Tree Draw Deck
• Phylodendron
• ARB
• unrooted
• DAMBE
• TREECON
• Mavric
• TreeExplorer
• TreeThief
• Bionumerics

Sequence management/job submission

• PARBOOT
• Random Cladistics
• Tree Gardener
• GDE
• MUST
• DNA Stacks
• SeqPup
• ARB
• BioEdit
• Singapore PHYLIP web interface
• PHYCON
• Bionumerics

Teaching about phylogenies

• Phylogenetic Investigator

Unix (source code in C or executables)

PC's

... under Windows

... under DOS or in a Windows "DOS box"

Macintoshes or PowerMacs

VMS executables or C sources with VMS compilation support

e-mail or Web servers that can analyze data for you

• Unix (source code in C or executables). I have included programs that are available as C source code because most Unix workstations have a C compiler. (A few programs with FORTRAN source code are included too).

  PHYLIP PAUP* Fitch programs Phylo_win ODEN TreeTree GCG Wisconsin Package SeqPup Lintre RSVP Microsat OSA TREE-PUZZLE AMP fastDNAml MOLPHY PAML SplitsTree PLATO STATGEOM PHYLTEST PARBOOT TreeAlign ClustalW MALIGN GeneDoc COMPARE TheSiminator Seq-Gen TreeTool GDE sog TreePack

  Phylodendron Treevolve and PTreevolve PSeq-Gen njbafd gmaes GCUA DERANGE2 LVB BIONJ TAAR ANCML QDate Bootscanning Package Ctree SOTA PASSML TOPAL reticulate RecPars ARB BIOSYS-2 RAPD-PCR package TreeCons Diversi DISTANCE Darwin sendbs partimatrix BAMBE nneighbor unrooted

  ROSE weighbor PhyloQuart QR2 VeryfastDNAml LARD puzzleboot Willson quartets programs POY RIND TipDate RRTree Fels-Rand PAL Mavric dnarates CLINCH UO Arlequin vCEBL TrExMl HY-PHY Genie Vanilla PHYCON qclust fastDNAmlRev RevDNArates BRANCHLENGTH TCS CONSEL

• PC's
  • as Windows executables (not counting executing in a "DOS box")

    PHYLIP PAUP* Tree Gardener TREECON GDA SeqPup MOLPHY WET GeneDoc COMPONENT TREEMAP COMPARE RAPDistance TreeView Phylodendron Molecular Analyst Fingerprinting POPGENE TFPGA Ctree GeneTree MVSP RSTCALC Genetix NJplot unrooted Arlequin DAMBE

    DnaSP PAML LVB DNASIS minspnet BioEdit ProSeq RRTree Fels-Rand PAL WINCLADA SECANT Nona DNASEP SEPAL Phylogenetic Independence vCEBL HY-PHY TreeExplorer Genie Vanilla MEGA TNT GelCompar II Bionumerics TCS

  • under DOS (MSDOS, PCDOS) or in a Windows "DOS box"

    PHYLIP PAUP* MEGA Fitch programs Hennig86 MEGA RA Nona TurboTree Freqpars Fitch programs TREECON Microsat DISPAN RESTSITE NTSYSpc METREE Hadtree, Prepare and Trees PHYLTEST RAPDistance

    DIPLOMO TREE-PUZZLE ABLE ClustalW MALIGN GeneDoc COMPARE CMAP Random Cladistics CoSta njbafd GEOMETRY PDAP PICA95 REDCON TAXEQ2 BIONJ ANCML REAP

    MVSP Lintre BIOSYS-2 RAPD-PCR package Diversi T-REX sendbs K2WuLi homoplasy test weighbor POY TreeDis QUARTET2 Network CLINCH Gambit MEAWILK qclust CONSEL

• Macintosh or PowerMac executables

  PHYLIP PAUP* CAFCA MacT TreeTree SeqPup Microsat TREE-PUZZLE fastDNAml MacClade Spectrum SplitsTree PLATO AutoDecay RASA ClustalW TREEMAP CAIC COMPARE PA Bi-De SEQEVOLVE TheSiminator Seq-Gen End-Epi

  StratCon CONSERVE TreeView NJplot DendroMaker MUST DNA Stacks Phylogenetic Investigator Tree Draw Deck Phylodendron TreeRot Treevolve and PTreevolve PSeq-Gen Molecular Analyst Fingerprinting BIONJ GCUA ACAP GeneTree QDate LVB T-REX unrooted GeneStrut COMPONENT Lite weighbor

  Modeltest PAML LARD MATRIX Willson quartets programs ALIGN CodonBootstrap DNASIS TipDate RRTree MacroCAIC Fels-Rand PAL RadCon TreeEdit Arlequin vCEBL HY-PHY TreeThief Genie Sequencer Vanilla TCS MrBayes

• VMS executables or C sources with VMS compilation support. (Many of the programs listed under Unix above have C source code which can also be compiled under VMS).
  • PHYLIP
  • MARKOV
  • TREE-PUZZLE
  • fastDNAml
  • TreeAlign
  • ClustalW

Microsatellite data

• RSTCALC
• njbafd
• Microsat

RAPDs, RFLPs, or AFLPs

• tfpga
• RAPD-PCR
• RAPDistance
• Molecular Analyst Fingerprinting
• GelCompar II
• Bionumerics

Continuous quantitative characters

(under construction: coming soon)

• CONSEL (8 March 2002)
• MrBayes (2 January 2001)
• TCS (28 December 2000)
• BRANCHLENGTH (25 December 2000)
• rate-evolution (24 December 2000)
• RevDNArates (24 December 2000)
• fastDNAmlRev (24 December 2000)
• GelCompar II (22 December 2000)
• Bionumerics (21 December 2000)
• PHYCON (18 December 2000)
• TNT (17 December 2000)
• Vanilla (16 December 2000)
• Sequencer (15 December 2000)
• TreeThief (14 December 2000)
• Genie (14 December 2000)
• TreeExplorer (4 December 2000)
• HY-PHY (2 December 2000)
• TrExMl (14 November 2000)
• vCEBL (3 November 2000)
• MEAWILK (2 November 2000)

• puzzleboot (6 July 2001)
• TCS (22 January 2001)
• Nona (3 January 2001)
• GCG Wisconsin Package (2 January 2001)
• TheSiminator (2 January 2001)

• There is one phylogeny software list even more complete and up-to-date than this one: a more recent version of this list. If you are reading this on the web pages at our server evolution.genetics.washington.edu, you are reading the most up-to-date version. But if you are reading a version stored anywhere else, you might want to look here instead.
• The University of California Museum of Paleontology page of Phylogenetics Software Resources at http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html. Few programs are listed, but there is a very nice list of software lists there.
• The BioCatalog phylogeny page at the European Bioinformatics Institute, located at http://corba.ebi.ac.uk/Biocatalog/Phylogeny.html
• The Institut Pasteur in Paris has the Bio NetBook, a search facility for biocomputing resources. It is located at http://www.pasteur.fr/recherche/BNB/bnb-en.html. Programs for phylogenies can be found by, for example, selecting software from the Resource Type list and evolution from the Biological Domain list without selecting any Organism.
• A brief list of programs at the Willi Hennig Society's home pages. It reflects a rather different worldview, centered on the parsimony method.
• Classification and clustering programs available for free by network are described in a useful Web page from the Classification Society of North America at http://www.pitt.edu/~csna/software.html. Note, however, that inferring phylogenies and making clusters are different tasks; the software described on that list will be of most use to people who are trying to cluster or classify but not to infer phylogenies.
• Genamics, a company located in Hamilton, New Zealand, maintains the SoftwareSeek searchable index of bioinformatics software at http://genamics.com/software/index.htm in a number of categories. One of them is Phylogenetic Analysis. They have a reasonably large number of entries under that heading, though it also includes some statistical genetics software that is really not phylogenetic. Their listing has links to the web sites of the software; for those programs that are not available by Web they maintain copies for download at their server.
• David Robertson of the Department of Zoology, University of Oxford has a very informative web site at http://grinch.zoo.ox.ac.uk/RAP_links.html listing programs and their web sites that test for the presence of recombination or hybridization events in DNA sequence data. It lists some programs that are covered here, and others that are outside the scope of these web pages.
• Georg Fuellen at the University of Bielefeld, Germany, has a very good page on Multiple Alignment Resources at http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.
• Don Gilbert, of the Department of Biology of the University of Indiana, has a good web page on Free Software in Molecular Biology for Macintosh and MS Windows computers at http://iubio.bio.indiana.edu/soft/molbio/Listings.html. It lists some popular packages and all packages and programs kept at the IUBio ftp server (see our description of that server). Unfortunately the web links on that page are not active so the addresses must be retyped by hand.
• Andrea Hansen, of the Universität Braunschweig, Germany, has created the bioinformatik.de index of resources. It includes a list of software located at http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software. The phylogeny programs listings there are located within the categories for different operating systems.
• The National Biotechnology Information Facility has a list of phylogeny programs (including some population genetics programs as well) at http://www.nbif.org/links/7_1_1_12_2.php.
• The list of phylogeny software compiled by David Maddison and Wayne Maddison as part of their "Tree of Life" project on the World Wide Web. Its URL is: http://phylogeny.arizona.edu/tree/programs/programs.html. This list has not been updated in a while.
• Dan Jacobson posted an extensive list of biological software and database sites at http://www.bis.med.jhmi.edu/Dan/software/biol-links.html. It has not, as far as I know, been updated in a while.

To first page of main software listing

... to the PHYLIP home page